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Title: Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis

Abstract

Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. In order to identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F 1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 x A4) x (AP13 x VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 x 100 bp) sequencing on the Illumina HiSeq2000 platform. Furthermore, mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense- related genes, including the nucleotide binding site-leucinerich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can bemore » a valuable resource for developing molecular markers for rust resistance. Finally we identified the rust-resistant genotypes and gene transcripts which can expedite rust-resistant cultivar development in switchgrass.« less

Authors:
 [1];  [2];  [3];  [3];  [4];  [5];  [1]
  1. Samuel Roberts Noble Foundation, Ardmore, OK (United States). Forage Improvement Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Dept. of Energy
  2. Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division; Dupont Knowledge Center, Telangana (India). Dupont Pioneer
  3. Samuel Roberts Noble Foundation, Ardmore, OK (United States). Computing Services
  4. Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Dept. of Energy
  5. Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1334446
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The Plant Genome
Additional Journal Information:
Journal Volume: 8; Journal Issue: 2; Journal ID: ISSN 1940-3372
Publisher:
Alliance of Crop, Soil, and Environmental Science Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Serba, Desalegn D., Uppalapati, Srinivasa Rao, Mukherjee, Shreyartha, Krom, Nick, Tang, Yuhong, Mysore, Kirankumar S., and Saha, Malay C.. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis. United States: N. p., 2015. Web. doi:10.3835/plantgenome2014.10.0075.
Serba, Desalegn D., Uppalapati, Srinivasa Rao, Mukherjee, Shreyartha, Krom, Nick, Tang, Yuhong, Mysore, Kirankumar S., & Saha, Malay C.. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis. United States. doi:10.3835/plantgenome2014.10.0075.
Serba, Desalegn D., Uppalapati, Srinivasa Rao, Mukherjee, Shreyartha, Krom, Nick, Tang, Yuhong, Mysore, Kirankumar S., and Saha, Malay C.. Mon . "Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis". United States. doi:10.3835/plantgenome2014.10.0075. https://www.osti.gov/servlets/purl/1334446.
@article{osti_1334446,
title = {Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis},
author = {Serba, Desalegn D. and Uppalapati, Srinivasa Rao and Mukherjee, Shreyartha and Krom, Nick and Tang, Yuhong and Mysore, Kirankumar S. and Saha, Malay C.},
abstractNote = {Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. In order to identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F 1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 x A4) x (AP13 x VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 x 100 bp) sequencing on the Illumina HiSeq2000 platform. Furthermore, mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense- related genes, including the nucleotide binding site-leucinerich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Finally we identified the rust-resistant genotypes and gene transcripts which can expedite rust-resistant cultivar development in switchgrass.},
doi = {10.3835/plantgenome2014.10.0075},
journal = {The Plant Genome},
number = 2,
volume = 8,
place = {United States},
year = {Mon Mar 16 00:00:00 EDT 2015},
month = {Mon Mar 16 00:00:00 EDT 2015}
}

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